org.geworkbench.bison.datastructure.bioobjects.microarray
Class CSMarkerValue

java.lang.Object
  org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable, DSMarkerValue, DSMutableMarkerValue

Direct Known Subclasses:

CSExpressionMarkerValue, CSGenepixMarkerValue, CSGenotypicMarkerValue

public abstract class CSMarkerValue
extends java.lang.Object
implements DSMutableMarkerValue

Title: Plug And Play Framework

Description: Architecture for enGenious Plug&Play

Copyright: Copyright (c) 2002

Company: First Genetic Trust

Version:

1.0

Author:

Andrea Califano

See Also:

Serialized Form

Field Summary

protected float	confidence Positive values are normal, negative values are masked.
protected static float	m_threshold
protected static float	MISSING Value which is assigned to the field confidence to indicate that the marker value is marked as "missing".
protected static float	p_threshold Used to define how present/marginal/absent calls should be made based on the call p-value: p-value < p_threshold --> Present p_threshold <= p-values < m_threshold --> Marginal p-value >= m_threshold --> Absent
protected float	value

Constructor Summary

CSMarkerValue()
Default Constructor

CSMarkerValue(CSMarkerValue m)

Method Summary

boolean	equals(java.lang.Object obj) Compares two expression markers
double	getConfidence() A value indicating our confidence in the measured signal.
char	getStatusAsChar()
double	getValue() Return the signal measurement for this spot.
boolean	isAbsent()
boolean	isMarginal()
boolean	isMasked() This method returns whether this marker should be temporarily ignored by analytical tools
boolean	isMissing() Check if the mesurement for this spot is classified as "missing".
boolean	isPresent()
boolean	isValid() This method returns whether the marker is both unmasked and not undefined.
void	mask() Sets the mask bit to be temporarily ignored by analyses methods
void	setAbsent()
void	setConfidence(double c) Set the confidence level.
void	setMarginal()
void	setMarginalThreshold(double mThreshold) Set the cutoff p-value used for a Marginal call
void	setMissing(boolean flag) Set the status of this spot measurement.
void	setPresent()
void	setPresentThreshold(double pThreshold) Set the cutoff p-value used for a Present call
void	setValue(double s) Set the spot's value.
void	unmask() Resets the mask bit to be used by analyses methods

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue

deepCopy, getDimensionality

Methods inherited from interface java.lang.Comparable

compareTo

Field Detail

p_threshold

protected static float p_threshold

Used to define how present/marginal/absent calls should be made based on the call p-value: p-value < p_threshold --> Present p_threshold <= p-values < m_threshold --> Marginal p-value >= m_threshold --> Absent

m_threshold

protected static float m_threshold

MISSING

protected static final float MISSING

Value which is assigned to the field confidence to indicate that the marker value is marked as "missing".

See Also:

Constant Field Values

value

protected float value

confidence

protected float confidence

Positive values are normal, negative values are masked. MISSING indicates missing value.

Constructor Detail

CSMarkerValue

public CSMarkerValue()

Default Constructor

CSMarkerValue

public CSMarkerValue(CSMarkerValue m)

Method Detail

getValue

public double getValue()

Description copied from interface: DSMarkerValue

Return the signal measurement for this spot. For 2-channel data, this is usually the ratio of the 2 channels.

Specified by:

getValue in interface DSMarkerValue

Returns:

marker value

setValue

public void setValue(double s)

Description copied from interface: DSMutableMarkerValue

Set the spot's value.

Specified by:

setValue in interface DSMutableMarkerValue

Parameters:

s - the spot's value

setMissing

public void setMissing(boolean flag)

Description copied from interface: DSMutableMarkerValue

Set the status of this spot measurement. The measurement could be be any spot specific information. eg: Missing, Present, Valid and/or others

Specified by:

setMissing in interface DSMutableMarkerValue

setAbsent

public void setAbsent()

setPresent

public void setPresent()

setMarginal

public void setMarginal()

isValid

public boolean isValid()

Description copied from interface: DSMarkerValue

This method returns whether the marker is both unmasked and not undefined. As a result, there is no corresponding setValid method. Should likely be moved to MarkerValue

Specified by:

isValid in interface DSMarkerValue

Returns:

isAbsent

public boolean isAbsent()

isMarginal

public boolean isMarginal()

isPresent

public boolean isPresent()

isMissing

public boolean isMissing()

Description copied from interface: DSMarkerValue

Check if the mesurement for this spot is classified as "missing".

Specified by:

isMissing in interface DSMarkerValue

Returns:

presence

isMasked

public boolean isMasked()

Description copied from interface: DSMarkerValue

This method returns whether this marker should be temporarily ignored by analytical tools

Specified by:

isMasked in interface DSMarkerValue

Returns:

mask

public void mask()

Description copied from interface: DSMutableMarkerValue

Sets the mask bit to be temporarily ignored by analyses methods

Specified by:

mask in interface DSMutableMarkerValue

unmask

public void unmask()

Description copied from interface: DSMutableMarkerValue

Resets the mask bit to be used by analyses methods

Specified by:

unmask in interface DSMutableMarkerValue

getStatusAsChar

public char getStatusAsChar()

getConfidence

public double getConfidence()

Description copied from interface: DSMarkerValue

A value indicating our confidence in the measured signal.

Specified by:

getConfidence in interface DSMarkerValue

Returns:

confidence

setConfidence

public void setConfidence(double c)

Description copied from interface: DSMutableMarkerValue

Set the confidence level.

Specified by:

setConfidence in interface DSMutableMarkerValue

Parameters:

c - confidence of spot's measument

setPresentThreshold

public void setPresentThreshold(double pThreshold)

Set the cutoff p-value used for a Present call

Parameters:

pThreshold -

setMarginalThreshold

public void setMarginalThreshold(double mThreshold)

Set the cutoff p-value used for a Marginal call

Parameters:

mThreshold -

equals

public boolean equals(java.lang.Object obj)

Compares two expression markers

Specified by:

equals in interface DSMarkerValue

Overrides:

equals in class java.lang.Object

Parameters:

m - MarkerValue marker to be compared to

Returns:

boolean equality